Documentation

Basic usage information for HMMER2GO can be obtained by executing the program with no arguments.

$ hmmer2go
Available commands:

  commands: list the application's commands
      help: display a command's help screen

  fetchmap: Download the latest Pfam2GO mappings.
    getorf: Run EMBOSS getorf and extract the reading frames.
   map2gaf: Generate association file for gene and GO term mappings.
  mapterms: Map PFAM IDs from HMMscan search to GO terms.
pfamsearch: Search terms against Pfam entries and create a custom HMM database.
       run: Run HMMscan on translated ORFs against Pfam database.

There is a help option available to all commands for getting specific usage information. For example, to get usage information for the hmmer2go getorf command, we can run the following command:

$ hmmer2go getorf [-acilostv] [long options...]
-i STR --infile STR     The fasta files to be translated
-o STR --outfile STR    A file to place the translated sequences
-l INT --orflen INT     The minimum length for which to report an ORF
-a --all                Annotate all the ORFs, not just the longest
                        one
-t INT --translate INT  Determines what to report for each ORF
-s --sameframe          Report all ORFs in the same (sense) frame
--nm --nomet            Do not report only those ORFs starting with
                        Methionine
-c --choose             Pick only one ORF to report if multiple of
                        the same length are found
-v --verbose            Print results to the terminal

The full documentation for each command can be accessed by specifying the manual option.

$ hmmer2go getorf --man